Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease. African American women are disproportionately affected and the etiology is believed to be a combination of genetic and environmental factors. The natural history typically includes diverse organ system involvement and a chronic course punctuated by flares. Multiple studies have demonstrated that monocyte function is aberrant in SLE and this is significant because monocytes can persist in tissues as differentiated macrophages and mold adaptive responses, thus producing a cascade of effects as a consequence of their aberrant function. Macrophages form the initial lesion in atheromatous disease, associated with the major cause of death in SLE and macrophage infiltration into the kidney is specifically associated with increased morbidity and mortality. These form the rationale for the study of SLE monocytes. We specifically hypothesize that the SLE disease process drives an altered epigenome in monocytes and this contributes to disease perpetuation and end organ manifestations. An altered potential for expression could lead to aberrant monocyte migration or inflammatory mediator expression. Pathologic responses to common innocuous stimuli, such as viruses could ensue as a result of an altered epigenome. This proposal will examine the epigenetic landscape of SLE monocytes and begin to identify pathways that are associated with altered histone modifications. Two opposing histone marks will be examined by ChIP-Seq, H3K4me2 and H3K27me3. We have preliminary data demonstrating altered H4 acetylation in SLE patient monocytes compared to controls. Network analysis of the gene set with altered histone modifications demonstrated nodes of biological relevance, including known inflammatory pathways. A second epigenetic feature, non-coding RNAs, will be examined on an exploratory basis. Preliminary data demonstrate tissue-specific antisense RNA upstream of the TNF1 gene which is associated with binding of a transcriptional repressor. Long mRNA-like non-coding RNAs will be examined and a novel ChIP-Seq approach, using S9.6, used to explore the structure of the potential regulatory RNAs. The S9.6 antibody will be used to identify DNA:RNA hybrid structures and this will be used to filter the non-coding RNAs identified bioinformatically. One of the major goals of this application is to begin to transition to a mechanistic examination of the alterations to the epigenome. We hypothesize that the disease itself drives most of the alterations to the epigenome, however, an existing SNP database on the same SLE cohort will be used to examine potential SNP associations with altered histone modifications. SNP analysis on RNA-Seq and ChIP- Seq data will allow allele-specific quantitation on controls, as a foundation for the SLE samples. This proposal will examine the epigenome in SLE and begin to examine potential causes and consequences. Collectively, these approaches will further our understanding of SLE and may develop a new paradigm for the understanding of the chronicity of autoimmune disease in general.